Equestria Girls: The New Doctor Episode Two: The Princess and the Crown

by zZ Sky Ninja Zz

Rating: everyone
Tags: Other, Adventure, Crossover, Human, Doctor Whooves, Twilight Sparkle, Main 6, My Little Pony: Friendship is Magic
Length: 8408

Episode 2 of EQG: The New Doctor. With a request from Velvet to check out a high school that Twilight will be attending, the Doctor is thrown into a new adventure with a different Twilight, strange energy sources and reuniting with old friends.

After the Doctor saved the world and got a new companion, Twilight Sparkle, he has been told she is moving. Her mother Twilight Velvet has a request for him. To go to check out the new school Twilight will be attending. But when he gets there he is thrown into a new adventure where he meets a strange Twilight, as well as an energy source in this school. Meeting old friends and helping bring together friends, the Doctor is in for an adventure even he has never done.

Published 2014-02-19 00:50:05 UTC
Last updated 2014-07-24 21:16:21 UTC

Prologue

"This is amazing!" Twilight exclaimed as she wondered through the TARDIS corridors. "I could wander these corridors for days and not know half it's wonders!"

"Well, make sure you don't get lost Twilight" The Doctor said from the console room. "The library should be on your next right."

Twilight was getting excited, they had just dematerialized from her backyard and right now she was exploring the place where she would be throughout her adventures with the madman in a box. Twilight looked in the room where the Doctor told her to go and her jaw dropped at what she saw.

It was a library. But it wasn't any library she's ever seen, it was massive! With different floors and shelves stacked with books as far as the eye could see. Twilight couldn't believe that the TARDIS can store something this big. Her eyes had stars in them as she took it all in.

"There are.... there are no words!"

The Doctor grinned as he heard her say that. The TARDIS gave him a handy little function so he can keep an eye on Twilight to make sure she doesn't get lost. It's not good getting lost around here. He spoke in the intercom knowing Twilight can hear him.

"Like it? Well, what's there is yours to read. These are books from all over the universe, well.... my universe anyway."

Twilight shook out of her state. "Wouldn't they have some weird language I can't read?"

"One step ahead Ms Sparkle, these books have been modified. Whatever language the reader uses in your case English. The texts in the books then translate to the readers eyes."

"Wow." Twilight whispered.

"Knock yourself out."

Twilights eyes shone like she was a kid again. She laughed and started bouncing up and down. "WOOHOO!"

She ran up to the nearest shelf and grabbed a handful of books, she placed them on a nearby table. She kept on doing this with other shelves.

"This is amazing! Lot's of books on lot's of species. This beats any university library!"

But then two books caught Twilights eye. One was on a podium and the other was behind one of the shelves and was bright blue.
Frowning, she took out the blue book and blew on the dust. Coughing a little from the dust, she read the title.

TARDIS MANUAL

"Why does the Doctor have this behind all the others? Surely he must keep it on him at all times?"

A light bulb flashed in Twilights head. "Hey, if I read this, maybe I can try flying this thing. How hard can it be? It's just a box!"
She set down that book as well and went to the one on the podium, the title was 'The Doctors Diary.' Slowly opening it, Twilight skimmed through a few pages and gasped. "So THAT'S your name."

She kept on skimming, the words that stuck out the most were 'Gallifrey', 'Time War' and 'Time Lord.'

"What do these words mean? I heard Prisoner Zero calling him a Time Lord, is that what he is? He did say he's an alien. But why does he look so much human?"

Shaking those thoughts, she closed the diary. "I'll ask him later, right now I have a manual to read! Ugh, never thought I'd say that at this age."

Twilight sat down and opened the manual, managing to take in some of the knowledge but not a lot.

Three Hours Later

"Does that girl do nothing but study?" The Doctor wondered out loud as he was working on the console. Twilight had been gone for three hours still in that library. He was about to go get her when Twilight came in holding a blue book. "Well, look who decided to show up."

Twilight smiled. "Sorry Doctor, just found the manual."

The Time Lord blinked. "Manual?"

She then frowned. "Yes, the TARDIS manual. Did you even read this? I found it behind the other books."

Sweating a little, the Doctor stammered. "O-Of course I have! It's my favourite bed-time story."

Twilight looked at it. "I wanted to see if I could pilot the TARDIS, but all I know is starting it up, flying it and landing it."

The Doctor leaned on a railing in thought. "You. Are. Brilliant! I can teach you Twilight. C'mon, I'll show you the controls!"

Setting the book down, Twilight continued. "I also have questions. You said you were an alien, what species are you? Why do you look human?"

The Doctor smiled. "I'm a Time lord. And actually, Time Lords were created before humans, so you lot look like me!"

Twilight giggled a little. "Okay, aside from the two hearts, what can.... Time Lords do?"

"Well, we can regenerate."

Twilight frowned. "Like a lizard?"

"Sort of, whenever we're dying, we regenerate. It happens when we're wounded or old, healing us."

The Doctor then looked at her. "But in the process, it changes us. Every single cell is changed and we get a new body, new personality, new everything. Time Lords can regenerate twelve times."

Twilight was shocked. "So there has been more than one Doctor?"

The Time Lord nodded. "Which one are you?"

"Number eleven. Those people you saw at the hospital, those were my past incarnations. Number four to number ten."

Twilight closed her eyes. "How did you die last?"

The Doctors face turned serious. "Doing what I always do, saving the world. I absorbed a lot of radioactive energy to save one of my friends. I managed to hold it off long enough to say goodbye to old friends but doing that, when I regenerated I destroyed the TARDIS."

"So wait, when I first met you, you had just regenerated?"

The Doctor grinned. "Yes, gave you quite a scare didn't I?"

"What is the Time War?"

The Doctors face darkened at that, turning his back at Twilight he said. "I do not like to talk about that."

Twilight was surprised at her friends change of mood. "I'm-I'm sorry."

"It's okay, you didn't know."

Clapping his hands, he turned around to face her. "Right, so we need to land in your backyard, see if you can do it. Let's see if reading is as good as the real thing."

Twilight nodded and walked to the console. "So you're really 1200 years old?"

"No." The Doctor answered. "I'm actually 906, but can't blame me at the time. I was still regenerating and couldn't think straight."

Looking over the many buttons, Twilight continued. "So, if you're an alien, why are you not at your home planet? Why come here?"

The Doctor looked down. "Because I don't have one."

Shock was present all over Twilights face. "I'm sorry?"

"My home planet Gallifrey, is gone. In the Time War, it got burned. No more Gallifrey, no more Time Lords. There are no more Twilight, I'm the last one."

Right at that moment Twilight looked into his Obsidian Black eyes and saw a man who has seen a lot, full of pain and regret. But thee was also a hint of someone who loves adventure. That's when she realised how lonely he really is, all these adventures he told her about is probably because he doesn't want other planets to end up like his own, that gained him a new level of respect in her eyes.

Shaking his head, the Doctor smiled. "Ah well, I can't dwell on the past. Gotta move on, now onto your lessons."

He grabbed her hands to which she blushed slightly and guided them over the console. "Now what you do is grab this lever to start, these buttons right here to which date and you flick this stick over here."

Twilight looked at it. "What does it do?"

"Nothing!" The Doctor grinned. "But it's fun."

He then went to the doors. "We have arrived at a location Twilight."

Opening the doors, Twilight gasped in amazement. "We're in space!"

It's true. They were now observing the Solar System from the TARDIS doors, in Twilights eyes it was beautiful. To go where few people have been and look at the stars. "Wow."

The Doctor grabbed her. "Enjoy." He then pushed Twilight out.

Screaming, Twilight flailed about thinking she was suffocating but stopped when she realised she was still alive. "How am I breathing? There is no oxygen here."

The Doctor jumped out too. "Force field around the TARDIS, giving us oxygen and we get a great view."

He floated next to her. "So what do you think of travelling with me?"

"If this is what's in store, count me in!"

The Doctor then looked into her eyes. "It won't always be like this, it will also be dangerous."

Twilight frowned. "What do you mean?"

"I am known throughout the universe, and there are all kinds of species who want me dead. I help when I can, but sometimes it doesn't end the way I want it."

Grabbing his hand, Twilight whispered. "I will be there with you all the way Doctor, you won't do this alone."

"Thank you." The Doctor whispered back. "So, ready to see if you can land in your back-yard? I did promise your mother to bring you back at a set time."

Twilight nodded. "Splendid." He lead her back into the TARDIS and spun around. "Now, I've set the correct date so all you need to do is pull the lever."

"Like this?" Twilights hand grabbed the lever but the Doctor stopped her. "You forgot to flick the wiggly thing."

Groaning a little, she flicked it and it made a 'BOING' noise. The Doctor laughed. "See? Fun!"

Rolling her eyes, she flipped the switch and the TARDIS jolted, the engine starting up. "God so far Twilight, now push that button to put up the shields, we are going through the time vortex."

Nodding, Twilight pressed a button and she sweated a little. "How do you do this?"

"Not so easy is it? Still, for your first time you're doing great."

He then grabbed her other hand. "Flip that lever to apply the brakes so we can land."

She did so and the TARDIS stopped, the core stopped going up and down and the spinny thing stopped spinning. "Did we do it?"

The Doctor checked his watch. "Yep, and with a minute to spare."

They both exited to see Velvet in a robe smiling. "You're early Doctor."

She then turned to her daughter. "How was it?"

Stars were present in Twilights eyes. "It was amazing!"

Night Light came out yawning. "Well, tell me all about it."

He lead his daughter inside, Twilight babbling what she learned. Velvet smiled at the young Time Lord. "Thanks."

The Doctor smiled. "No problem, she's a great companion. Hey, maybe I can take you all on a holiday someday, to Barcelona."

Seeing Velvets confused face, he continued. "Not the country, the planet. Really great places, they have dogs who don't have noses!"

Laughing a little, Velvet said. "We'll pass for now, we have to pack up, that's why I wanted her back early. We're moving."

"Really? Just pack your stuff in here, I can take you to your new home."

Velvet rolled her eyes. "I think we would prefer doing it the 'old fashioned way' Doctor."

The Doctor pouted. "If you wanna be boring...."

"Alright, there is something I want you to do for me."

Looking at her, he said. "What is it?"

Velvet rubbed her arms. "Well, since we're moving, Twilight has to go to a different school. I know it's a stupid request but could you check it out for me please?"

The Doctor smiled. "Sure, what's it called?"

"Canterlot High."

Author's Note

That's a good prologue, it was something I wanted in episode one but what can you do? Next chapter, the Doctor will be visiting this school and meeting old friends. I'll give you guys more clues, his companions are not in the DW universe, they're EQG characters:

Two are sister (Travelled with 5th Doctor)

One's a teacher (Travelled with 8th Doctor)

Two are students (Travelled with 10th Doctor)

One student has an eye problem while the other has orange curly hair.

Tune in next time to see the beginning of episode two.

Favourite, Follow, Review.

Safety and Peace and may the Gods of Budder protect you.

To Canterlot High!

"To Canterlot High!" The Doctor declared as he flipped a lever. He has heard of the school, since two of his companions here go to this school, but he had never seen it for himself.

The Doctor was in thought. "Hmmm..... I wonder if those two still go to that school." He then grinned. "I'll find out soon enough! Avante!"

He landed the TARDIS and stepped outside. "Hm, seems to be empty."

He was right. There was no one in sight, must have been class time. The Doctor looked around and for the first time, saw the very school two of his companions went to.

"Well, time to explore inside." The Doctor thought. Before he got out, he coughed up a little gold energy.

"I've got to stop doing that." He said. Yes, he was still regenerating. The reason it has taken so long is because instead of resting like he should be, he had been saving the world.

As he entered the school, he looked at his reflection in the window. "Ah, look at that. White hair, yellow skin, black eyes."

The Doctor leaned in closer. "I do like the eyes, very nice touch."

Suddenly the bell rang and he was stuck in a crowd of students. Trying to get through, he bumped into someone.

"Oh, sorry!"

The Doctor opened his eyes which then widened when he saw who he bumped into.

It was a girl with blond hair and gray skin. She also had yellow eyes but one was a little lazy, beside her was a girl with yellow skin and orange curly hair. She also had blue eyes. Their names were Ditzy Doo and Carrot Top.

Carrot Top frowned. "Are you new here? I don't think I've seen you round before."

Shaking out of his shocked state, the Doctor cleared his throat. "Uh yes, I'm..... Smith. John Smith."

Ditzy Doo gasped. "That's weird! We knew someone who went by that name. I even dated him!"

Laughing nervously, he replied. "It's a common name."

Shaking her head and smiling, Carrot Top helped them up. "Welcome to Canterlot High John."

The Doctor smiled widely as he watched his past companions leave, he hasn't seen them since his tenth incarnation and it was wonderful seeing them again. He then decided to ask where the principals office is so he can know more about the school.
The Time Lord decided to ask a teacher, so what better place than a classroom. He entered one. "Excuse me miss, but do you know where the principals office is?"

The woman turned around and the Doctor gaped. It was Cheerilee. He hadn't seen her since his eighth form, she looks so much different. She smiled. "Yes, it's on the third door on your right."

Cheerilee frowned. "Um, is there something wrong?"

"No no! It's just, I'm new here and it's always nice to meet a new face."

Nodding, she replied. "It is. May I know your name?"

The Doctor grinned. "John Smith."

Cheerilee was so shocked she dropped some books in the process. "That's what HE called himself."

Laughing a little, he quickly darted out the door leaving a shocked Cheerilee. "It couldn't be him, could it?"

giggling a little, she continued. "Don't be ridiculous Cheerilee. He may be out of this world but he can't change his face. Certainly not to a teenager."

Managing to find his way, before coughing up more energy, the Doctor knocked on the door. "Come in."

He walked in to find the principal with her back turned to him. "How can I help you?"

Smiling, the Doctor said. "I'm John Smith, I'm new here. Just wanted to know what's in store for me here."

He then gasped when she turned around, he almost didn't recognize her. Celestia. It's been over a decade since he last saw her.
She and Luna were teenagers when he last saw them which was in his fifth form. "Funny, I knew someone who called him that."

"Yes, who is this person? He seems quite popular."

Smiling a little, she explained dreamily. "He was literally out of this world. Always kind, selfless, let nothing get him down and was generally a great guy."

Celestia then giggled a little. "But his fashion sense was atrocious."

This insulted the Doctor. "What do you mean?"

"Well, the fact he wore cricket stuff and a weird coat, not to mention he wore a stick of celery on his lapel."

The Doctor stuttered. "W-Well maybe cricket outfits were in that year."

"Yes..." Celestia muttered. The Doctor saw a book on her table and flipped through it. "Heh, sad ending."

This shocked Celestia. "How did you do that?"

"Do what?" The Time Lord replied innocently.

"The fact you were able to skim through the book and read it. I just bought that book which came out today!"

The Doctor shrugged, smirking. "I can fast read."

Seeing a leaflet (or brochure if you're American) on the table, he picked it up. "Never mind, I'll just read this so I know what's in store. Good day Tia."

Celestia gasped as he left. "Only three people called me that. Luna, Discord and....... him."

She glared at the door. "I'll figure you out Mr Smith."

The Doctor laughed out loud as he walked through the hallway. "Oh, the look on her face. I wonder if anyone figured out who I was. Probably not, but it's for the best. They left for a reason."

A piece of headwear caught his attention, he was passing a Drama classroom when he saw..... a fez.

"Ooooooohhhh..." The Doctor dashed over to it and lifted it before putting it on. He checked himself in the mirror and grinned. "Yep, fezzes are cool!"

He then decided he has seen enough, so with no other reason, the Doctor departed to his TARDIS before bumping into a yellow skinned girl. "Oh gosh, I'm so sorry!"

The Doctor looked up at the girl, he saw she also had light pink hair and cyan eyes. She was also holding papers. "I'm sorry mister, it was an accident I swear."

Dusting himself, the Doctor smiled. "No harm done, oooohhh look an animal shelter!"

He snatched a paper from her, scaring her a little. "Oooohhh animals, I love animals! Well, okay maybe not sheep. Honestly, they're so rude when you try to talk to them."

The girl was now shaking. "W-What do you mean?"

"Oh, I speak sheep. I speak every language and I don't believe I know your name."

The girl mumbled something which the Doctor understood. "Fluttershy! Great name. Surprisingly fitting for a girl like you."

Fluttershy walked away. "Umm..... I have to go now.....?" She asked his name.

The Doctor smiled. "John Smith, or Smithy if you like."

"G-Goodbye John."

Sighing happily, the Doctor made his way to the TARDIS to tell Velvet the good news. As he got to the console, he was about to pull the lever when the screen alerted him. Curious, the Time Lord pulled it down to his eye level to see the words.

UNKNOWN ENERGY SOURCE DETECTED

The Doctor grinned at that. "A new source of energy that even Sexy here doesn't know about. Off to investigate!"

With that thought, he ran out the TARDIS and activated his Sonic and followed it to the energy source, which was coming from the statue.

"How can an ordinary statue be home to this kind of energy radiation?" The Doctor mused, he quickly scanned it with the Sonic and put it on a permanent setting deep within the software so no matter what, the calculations were still going on. After he did that, the Sonic started beeping and when the Doctor turned it, it beeped faster as he turned it towards the school. "Hmm.... maybe there is more of this energy radiation, I need some more to make the results go by faster. Ah well, Avante!"
So once again, the Doctor went back into the school to continue his investigation. The first thing he should do is rest- NO! No time for resting, Time Lords do not rest. He coughed up some more energy while other students looked at him weirdly. But the Doctor didn't care.

"Maybe one of the lockers will have something useful." The Doctor mused. So he took out his Sonic and worked the code on a random locker, he quickly opened it only to find nothing of use to him. Suddenly, he felt something bump into him. He quickly closed it and looked down. "Woah, you okay?"

His eyes went to confused when he saw.... Twilight? No, this one was different to the one who travels with him. For one thing, his Twilight didn't look freaked out about her very environment as well as looking at his hand like it's a tentacle, but she placed her fist on his hand anyway, narrowing her eyes as she slowly opened it as the Doctor helped her up. Twilight then nodded silently and watched the Doctor walk away, but not before he heard the dog say. "I don't think this is a castle."

The Doctor frowned. "Either that dog spoke English or my ability to speak with dogs is very clear now."

"But who was that Twilight?" He got his answer when his Sonic started beeping, in the direction Twilight was. "Hmm.... She has the same radiation as the statue. Aha! I need to find Twilight!"

So the Doctor then ran to catch up to Twilight, pushing through crowds and started his new adventure, in Canterlot High.

Author's Note

That's a wrap. Alright, don't expect an update for a while since I'm focusing on other stories. For the people who guessed the Doctors past companions correctly, give yourself a nice Jaffa Cake, know what? I'll give you guys a nice Jaffa Cake. So, I know I'm gonna work on this story anyway but.... I'll work on my other stories.
Favourite, Follow, Review.
Safety and Peace, and may the Gods of Budder protect you.

Meeting New People and Trying to Find More Data (Along with what appears to be a lot of sexual word choices....)

The Doctor was looking around for this mystery Twilight to see if he can scan her, but so far he wasn't having any luck.

"How hard is it to find that girl?" He muttered as he walked into what seemed to be the gymnasium. As the Time Lord walked in he saw a bunch of people, a pink girl with pink hair blowing up balloons and two boys who looked to be freshmen, but he wasn't sure. The other girl had red/yellow hair and piercing cyan eyes and the last girl was a familiar face.

'Huh. That was the girl I met when Prisoner Zero was running about.'

The pink girl looked at him and waved. "Hi there!"

All the attention was on him now and the familiar girl, who looked like a cowgirl, gasped in shock. The girl she was arguing with glared at him. "Beat it, this doesn't concern you."

The two boys shouted. "Yeah!"

The Doctor frowned. "I believe this does. I'm looking for someone. A girl, she has purple hair and purple skin."

The pink girl shot her hand in the hair. "Yes miss...... I'll call you Pinkie."

The girl beamed. "That's great 'cos that's my name! Well, there was a girl that came in here earlier!"

Pinkie then appeared behind him, and whispered in his ear. "Sheeee's psychic."

She then took out her clipboard. "She signed up to be Princess of the Fall Formal."

"WHAT?" The cyan eyed girl yelled as she snatched the board. "I know, her writing is really bad."

The girl then glowered. "Where is this Twilight Sparkle?"

The Doctor noticed his Sonic was reacting towards the girl, he flicked it out and started to scan her. The boys didn't like that. "Get away from Sunset Shimmer!"

They charged at him but the Doctor just sidestepped out the way making the two crash, Sunset shoved him. "Get away you freak!"

Pinkie Pie bounced to the cowgirl. "Applejack..... you okay?"

"Hm. She seems to be in shock."

Pinkie Pie looked at him. "I don't think I've seen you before."

"I just moved here." The Doctor lied.

"Ooohh!" Pinkie Pie beamed. "So anyway, about Twilight. She came in here and I knew she was psychic because she knew our names!"

The Doctor looked at the door. "I have to go now."

"WAIT!"

He turned around. "What's your name stranger?"

"John Smith."

Pinkie Pie smiled and waved. "Bye John!"

As he left, Pinkie Pie noticed that Sunset was gone too. "It was him!"

She turned to Applejack. "Huh?"

Applejack pointed at the door which the Doctor left. "I saw him last year at the hospital! When those weird things were around. And Twilight was there too! But why was he wearing a fez?"

The party girl shrugged. "I dunno. Maybe fezzes are cool?" Pinkie Pie then started shaking and moving all weird. "Oooohhh, my Pinkie sense is acting up. Haven't had one of those in a while."

The cowgirl looked at her. "What does it mean?"

"It means that something I would never see coming is gonna happen."

Applejack at this point tuned out the party girl and glared at the door. 'Yer gonna answer a lot of ma questions John.'

Outside, Sunset had just finished speaking with Twilight and blinked when her henchmen came stumbling wrapped in streamers, she ripped the streamers off them. "I want you to follow that girl. Bring me something I can use against her just like that last girl who thought she could challenge me."

The boys, known as Snips and Snails, saluted. "You got it Sunset Shimmer."

She then turned and muttered to herself. "Once the crown, and it's power, are mine. Twilight Sparkle will be sorry she ever set hoof into this world. Not that she'd be safe if she stayed in Equestria."

Sunset blinked when she heard Snips say. "Yeahhh.... an Equestria."

"What are you still doing here? GO!" She snapped. As she watched them run she yelled. "One more thing!"

They turned around. "Yes?"

She glared at the door. "I want you to also find out about that creep. There's something..... different about him than everybody else."

They saluted again. "Aye Aye!"

As they disappeared, Sunset heard a voice and cringed in fear.

"Soon you'll have the power, little pony."

Sunset shivered. "Who are you? Why won't you tell me who you are?" She has had this voice in her head ever since she was a filly, and it scared her to no end.

The voice chuckled. "Why do I need to tell you? I'm the one responsible for putting you on this path for power, imagine little pony. Power beyond your imagination."

Sunset cracked a shaky smile. "Yes, I can imagine it! It won't be long now. I just have to make sure Twilight Sparkle won't get the crown."

"That pathetic pony is the least of your worries. I'd keep an eye on the human you just met."

"What? That creep who pointed that... thing at me? Why him?"

The voice growled making Sunset whimper, luckily no one was around. "He is more than he seems. I have an idea who he is but I need a proper look at him to confirm it."

"W-What will you do if he is who you think he is?"

"I'll make sure to make him pay! I met him before and he's the reason I'm in this position!"

The voice stayed silent until eventually. "Make sure you get the crown. We are close.."

Sunset couldn't hear the voice and shivered. "That voice gives me the creeps."

She gasped when she saw marks on her hands, they looked ancient. But they disappeared when she blinked. "Must have been my imagination."

Drawing a deep breath, Sunset returned to her normal posture looking like nothing happened and walked down the halls.

In the school library, Twilight (Equestria Twilight, duh!) was in deep thought. Her dog, named Spike asked. "What's wrong Twilight?"

She sucked in a deep breath as she turned a page in a book. "It's that guy who helped me up today."

Spike grinned and nudged her. "Ooohhh, so you have a crush?"

"W-What? No!" Twilight turned deep red. "He just reminds me of someone...."

Spike looked down in thought. "Hmm..... you mean that clocksmith back in Ponyville?"

She clapped her hands. "Yeah! Shooting Star! It's strange though.... that guy looks like him in every way...." Twilight stared in space with a dreamy smile and a slight blush, to which Spike noticed. "Oh yeah. I can see that. Are you gonna do the same with what you did with Shooting Star?"

Twilight gulped. "What do you mean?"

"I mean when you break a clock on purpose so you can see him more."

Spike put a paw to his chin while Twilight blushed. "But you have a point. Didn't you see that stick in that guys hand? Looked just like the one Shooting Star uses, even has that.... mysterious aura around him."

The two just kept on researching stuck in their own thoughts about the Doctor.

Snips and Snails were discussing a plan. "Right, I go and spy on that Twilight girl and you go and spy on the new guy."

Snails grinned and nodded. "Got it."

They went their separate ways, Snips sneaked into the library and Snails went to look for the Time Lord.

"Where is that guy?" Snails thought to himself. His question was answered when he saw the yellow skinned alien looking through lockers. "C'mon, need to find more of that source."

Snails hid behind a pillar and frowned. "Source?" He took out his phone and started videoing the Doctor.

The Time Lord in question was cracking locks using his Sonic. "Doesn't seem I'll get much luck here. I need to find Twilight."

He then looked at his Sonic. "But when I went past Luna's office, the Sonic was going haywire. I need to find out what's making it do that."

The Doctor suddenly collapsed as he clutched his chest. "Agh! Don't do that!"

He also coughed up more regenerative energy. "No time to rest, I need to get back to the TARDIS."

But he then smirked as he pointed his Sonic Screwdriver in Snails direction. "Can't let THAT be on video can we?" The Sonic wirred loudly causing Snails phone to short circuit while the boy stared in shock.

"B-But how?" Snails watched the Doctor walk away. "I need to tell Snips." So he picked himself up and sprinted out.

Snip was waiting at the library door when Snails crashed into him. "Ow! Watch it you doofus!"

He then picked himself up. "Did you find anything?"

Snips grew concerned at the look of shock on his friends face. "You okay dude?"

"He.... he coughed up some thing..... he mentioned a.... Tardic?"

The short boy frowned. "Well, did you get anything?"

Snails showed Snips his broken phone. "He pointed a weird stick at me and broke my phone."

His friend gasped. "You don't think he's.... a wizard do you?"

"Yeah. It looked like he had a wand...."

"Let's tell Sunset Shimmer!"

The two boys sprinted to find their boss. Meanwhile, in the TARDIS, which the Doctor moved into a storage room. The Time Lord slid his Sonic into a slot in the console and watched the TARDIS try to crack the code on this source.

"Hmmm.... that Sunset Shimmer has a trace of energy that is familiar. It is ancient.... too ancient."

He shook his head and took out his Sonic. "I'll think about it later." He looked at his floor. "Maybe I should make the floor out of glass..... I'll put it on the back burner for now."
With that thought in his head, he noticed it was now night time and that no one was around. "Perfect, more time to investigate."

The Doctor felt his head and sighed. "I wish I didn't leave my fez in the TARDIS, ah well."

He looked around the school until he finally found what he was looking for. Vice Principal Luna's office, he quickly used the Sonic to turn the lock. As he opened the door, he was welcomed to a dark room, literally. The walls were midnight blue and almost everything was night time themed. "Lulu hasn't changed one bit."

He looked around and pointed his Screwdriver around looking for a rapid beeping. Eventually, he locked onto a crown in a glass casing which he noticed the star shaped jewel was glowing. "There you are, you beautiful thing."

He took out his glasses from his inner hoodie pocket and put them on. "Well, at least I kept one thing from my last incarnation."
As he inspected the crown, the Doctor scanned it with his Screwdriver and was shocked with the results.

"This can't be. He can't be back, I watched him go. I was the reason he's gone!"

He looked at his Sonic and saw it trying to process ancient letters but failing "That's impossible."

"Hey!"

He turned to see a suspicious Twilight. "Who are you and how did you get here?"

"I'm sorry."

Twilight raised an eyebrow. "What do you-"

He quickly ran to her and chopped her neck, her eyes rolled at the back of her head as she lost consciousness, she fell but the
Doctor caught her. "I'm surprised I still know how to do that, it's been centuries since I did that."

He looked at Twilight. "You're not my Twilight, I'm not even sure if you are human."

The Doctor forgot about scanning her as he carried her to the library. "If you're anything like my Twilight you love books."

He spotted a book bed and grinned. "Bingo."

Placing her on the bed, he noticed her dog was curled up next to her sleeping form. "I'm guessing you're not the Spike I know."

The Doctor stroked Twilights forehead. "I'll find out who you really are Twilight Sparkle, but I have a job to do."

So, he draped a blanket over Twilight and exited the library. "If that thing really is back, not only is this planet in danger, but the entire universe is too. All of them."

The Doctor sprinted to the TARDIS and prepared to have her process these calculations.

Author's Note

Chapter Wrap Up Chapter Wrap Up...... Oh hi. Now you may all notice, this Doctor is different, and you are correct. He's gonna be different to the actual 11th Doctor, but doesn't mean you should strike out chinny just yet. He will be in this fic in the future. Anyway, tell me what you think and who you think that voice was.

Favourite, Follow Review.

Safety and Peace, and may the Gods of Budder protect you.

The Plot Thickens

Chapter 4

As morning rose in the air, Twilight shot up gasping and panting. Spike fell off the bed and looked at her. "What's wrong Twilight?"
"That....... that guy! He was next to the crown. And....... did he knock me out?" Twilight proceeded to check herself. "Well, at least he didn't take advantage of me. Then again, if he IS Shooting Star he would never do something like that."

"Twilight?"

"Yes Spike?"

The dog reminded her. "The crown."

Suddenly remembering her reason for being in this world, Twilight got up. "Right, well it's time to work. Let's go Spike!"

The two ran downstairs to prepare for the day.

With the Doctor

The Time Lord had been up all night studying the calculations to try and see if he could confirm his fears. So far, no luck. "Maybe if I get more, the TARDIS can have an easier time."

Stepping out of his blue box, he decided to try his luck finding Twilight again. After forgetting to scan her last night, finding her was the Doctors number one priority. He checked his watch and saw it was almost afternoon. "Oh dear, I guess I lost track of time."

Deciding to try outside the school, the Doctor walked over to the place where he hears students usually go on their breaks. It was a
sweet shop that served in all various delicious treats. From donuts to brownies, they had it all. The Doctor decided to see what they had to offer.

The woman, who was called Mrs Cake smiled. "Welcome."

"Hello."

Mrs Cake gestured to the treats. "What would you like?"

The Doctor looked down. "Do you have fish fingers by any chance?"

The woman had a look of pure confusion. "Umm...... excuse me?"

"And custard?"

Mrs Cake stuttered a little, but saw the fifty dollar bill in his hands. The Doctor never really cared about money so just soniced the ATM and got a random bill. "I'll see what I can do."

The Doctor nodded, but when he turned around, he bumped into someone spilling their drink on them. "Oh, dear. I'm so sorry."

The boy chuckled. "Its okay. Accidents happen."

He then looked at the Time Lord. "Hey, you're that new guy aren't you? John Smith?"

The Doctor nodded. "Yes. That's me."

Extending his hand, the boy smiled. "I'm Flash Sentry. Nice to meet you."

Shaking the hand, the Doctor smiled. "Likewise."

Looking at his ruined shirt, Flash sighed. "It's not your fault. However, I have to clean this up now."

As he left, the Doctor didn't notice someone was in the line before him. So when he turned around, the Doctor bumped into said person and got a whole drink spilled on him. 'I still need to sort out the steering. It's still not right.'

"I'm so sorry!" The person said, who's voice was female as she went to pick up her now empty cup. The Doctor also tried to pick it up but stopped when the girls purple hand was placed on his own. He made eye contact and his eyes widened at who it was.
It was Twilight. Suddenly, he jumped up surprising the poor girl. "W-What's wrong?"

Taking out his Screwdriver, he showed Twilight his psychic paper. "Inspector of....... strange people. I need to scan you."

Hoisting the purple skinned girl upright, he quickly scanned her. 'Amazing. Her energy is much higher than that of Sunset Shimmer. Though, both are nothing compared to that crown. I believe I have everything I need.'

Twilight blushed at the close contact. This may not be him, but he still looked like her crush and was a little nervous. 'He acts just like the pegasus too! Who is he?'

The Doctor grinned. "All done. I can confirm that you are clean, fine and dandy. Bravo!"

Twilight smiled shyly. "I'm..... going to join my friends now."

The Doctor nodded as he watched her leave. 'What kind of life form are you Twilight? You're not human. I can say that much.'
With Twilight, she blushed as she twirled a lock of her hair. "Oooooh. Got a crush I see?"

The ex-alicorn blinked and looked at her friend Rarity. "What? No!"

Rainbow Dash scoffed. "Don't know why you would. He's a nutcase!"

"Rainbow!" Rarity scolded. "Don't be rude."

"Well, it's true! Have you seen him? He claims he can talk to animals, he has that stick with him and worst of all, he knows nothing about personal space."

Pinkie Pie stared at Rainbow Dash. "Are you mad because he beat you at football?"

"He got lucky!"

"I dunno Dashie. He clearly creamed you."

Rainbow Dash growled and slumped on her chair in a huff. She then noticed her friend Applejack was glaring at the Doctor. "What's wrong AJ?"

"It's him. The 'Raggedy Doctor'."

The girls were confused. "Isn't that a made up character by Apple Bloom?"

Twilight frowned. "I'm sorry?"

Rainbow Dash sighed. "About two years ago, Applejacks sister, Apple Bloom made an imaginary friend called the Raggedy Doctor. It's weird since she is way too old for that."

Applejack growled. "He ain't imaginary! Ah saw him that day when those.... things came here."

Fluttershy looked at her. "Um, if you don't mind me saying, but wasn't that a publicity stunt?"

The purple skinned human was now more confused. "Huh?"

Rarity looked at her like she had two heads. "You don't know? It was all over the news."

Twilight laughed nervously. "I guess I don't know."

Pinkie Pie raised her hand in the air. "Ooh! Ooh! Can I explain it?"

Sighing, Rarity nodded. "Well, about two years ago. There were these people who did these craaaazy things! Using these spaceships and cool special effects to add to it. Anyway, it only lasted about four hours before the ships all left."

Twilight thought. 'Hmmmm.... now that I think about it, I did see something on that computer about that sort of thing. But out of the pictures I've seen, it looks too crazy. Even for this world.'

"Yes......" Rarity blinked. "Anyway, it was all fake of course."

"It wasn't!" Applejack snapped. "That guy came in and chased them aliens away."

Rainbow Dash growled, like she's heard this a hundred times. "He's not real! The Raggedy Doctor is just someone your sister made up! The fact he looks like that guy is just a coincidence!"

The two girls were at each others faces at this point and the others just shook their heads, like this was a regular thing.

The Doctor heard everything. "Dammit. I need to be more careful in the future. Still, a trick? Now that's just crazy, even for the humans."

After getting his custard with a bunch of fish fingers in it, he walked away. But not before looking at Twilight one last time before leaving.

The girls (minus Pinkie Pie) had disgusted looks on their faces. "See? Nutcase."

Applejack groaned as she stood up. "Alright girls. We have gone off topic. Let's discuss the reason why we're all here."

The Doctor walked outside still thinking of those calculations when he bumped into some kids. "Oh dear, sorry."

The one with a bow stared at him in pure shock. He smiled and waved as he carried on his way. One of her friends said. "Apple Bloom? You okay?"

She quickly took her out her backpack and picked out a drawing. "Raggedy man!"

Scootaloo's eyes widened when she saw the similarities. "Woah, that is freaky."

"Come on! I need to tell Applejack!"

The Doctor coughed up some more energy in thought. "Hmmm..... the Fall Formal. I need to check that out, see if I can find any clues. But I need to find out about the event altogether. I know! Celestia could help me."

With that thought, the Doctor sprinted to the school wanting to know more about this. He ended up bursting into the staff room with eyes on him. "Um, hello."

Celestia cleared her throat. "Hello...... John. Students are not allowed in here."

Next to her was her younger sister, Luna. "Sister, who is this?"

Taking out his psychic paper, he showed it around."Hello, I'm not really a student, I'm inspector of...... upcoming social events. And I hear you have one tomorrow?"

Neither Celestia, Luna or Cheerilee was buying this but decided to comply. "Yes...... inspector."

Walking around, he noticed a bunch of pictures. "So, this Fall Formal, mind explaining it?"

"Yes. The Fall Formal is an event we have every fall along with other seasons such as the Spring Fling. It's like a prom in a way, and at we get the students to decide who will be the Princess of the Fall Formal."

Taking out a notepad to take notes, the Doctor nodded. "Does the...... Princess get anything?"

"Yes. The Princess is awarded with the crown that currently in my sister Luna' office. May I ask why you're asking these questions Mr Smith?" Luna gasped at that name as she finally had her suspicions. The Doctor threw the pad away. "Common question with these.... events....... Q and A, I thank you all for your time but I must take my leave."

He then spotted a plate of Jammy Dodgers. "I'll take these as payment." He grabbed the plate, put one in his mouth and the rest in his pockets. "Pleasure doing business."

As he left, one of the teachers said. "What just happened?"

Celestia was glaring at the door. 'Is it him? If so, why wait all these years to show up again?'

Outside, the Doctor was walking back to the TARDIS munching on Jammy Dodgers. 'Right, so what do I know so far? There's another Twilight, and based on the evidence she is not human. Also, there is a crown which may or may not host one of the most dangerous enemies I've faced of all time. None of which seem a capital idea in my case.'

Munching on more, he continued. 'Now, there is going to be an event tomorrow which, by the sounds of it, is a high school dance. And like a Prom Queen in my universe, there is a 'Princess'. Whoever wins gets the crown. Now, normally I would enter myself and try to win, but in this case I'm not female. Damn regeneration.'

His thoughts then returned to Twilight. 'She's my only chance. I may not know her but it seems that she knows me. Maybe I can convince her to give me it if she wins, since she seems to be competing with that other girl, what was her name? Sunset Shaker?'
Opening the doors to his blue box, he decided to go on a small trip so he can work out those calculations.

Ditzy and Carrot Top were walking down the hallway chatting when suddenly they heard a whirring noise. Both girls widened their eyes and looked at each other. "It's him!"

They sprinted to where they heard the noise and saw the TARDIS dematerializing.

"DOCTOR!!!" Ditzy yelled but it fell on deaf ears as the box was gone. Carrot Top blinked. "So, he's really back."

Ditzy nodded. "But we would've seen him by now, he's not hard to miss. A man in a suit with a brown trenchcoat, along with brown skin."

Carrot Top shook her head. "No. If he's here then it's not good news. What about that John guy? He looks like someone who would know."

"I guess.... but why is he back?"

The redhead shrugged. "Aide from that strange eyeball, nothing out of the ordinary has happened."

Meanwhile, Cheerilee was sorting through books when the Doctor came into her mind. 'He has to be back, I know I heard the TARDIS earlier. But..... why has he come back now? After all these years....'

Celestia and Luna were also pondering. "Okay, if he IS who we think he is, how? He looks way different and younger."
The headmistress groaned as she held her head. "I don't know, but it's him. I know it."

None of the Doctors companions in this universe knew he could regenerate so they all think he is still the same person they last saw.

Back in the TARDIS, the Doctor was analyzing the calculations and his fears were growing. "No. It can't be him. It just can't! If it is him then this whole universe is finished."

Meanwhile....

Sunset Shimmer had just told Snips and Snails her plan to ruin Twilights chance for the Fall Formal. She stiffened in fear when she heard the voice.
"Yes.... the plan is going smoothly. Soon I will be unleashed and away from this wretched prison!"

"B-But what are you going to do?"

"First, I will destroy the Time Lord who is the reason I'm even here! Then, I will enjoy wrecking havoc in the universe!"

The voice laughed loudly and Sunset whimpered. Perhaps she made a mistake doing this.... no! She has come too far to stop. The crown is so close. The plan just needs to come together.

Finally, the Doctor came back to the school about to find Twilight when he bumped into Flash Sentry. "Oh, hello Flash. What has gotten your panties in a bunch? Hmm...... nope. Never saying that again."

He suddenly felt woozy as he leaned on the wall. "No..... not now...... now is not the time."

Flash just saw gold energy flow out the Doctors mouth. "Did you just..? Never mind. Look, Sunset Shimmer is trying to make Twilight not compete for the Fall Formal."

"What? No, she HAS to!" The Doctor noticed scrap paper in the bin and took it out. "What are these?"

Flash looked at them. "Looks like someone cut out a person.... wait a minute....."

The Time Lord noticed the outline. "It's Twilight! Of course!"

Flash nodded. "Sunset Shimmer said she had photographic evidence, this must be the scrap!"

"We need to bring this to Luna!"

The Doctor dragged him. "Let's go, Avante!"

It took a while, but Luna was convinced Twilight wasn't responsible for the damage caused in the gym, but the dance had to be postponed. As she walked out, Twilight hugged both of them. "Oh! I can't thank you two enough!"

Flash decided to ask. "So, if you weren't already going with somebody, wanna come to the Fall Formal with me?"

Stepping in, the Doctor asked. "Um, Twilight I need to ask you about that."

The blue haired teenager was shocked. John liked Twilight too? Well, he wasn't giving up that easily. Suddenly, Twilight started panicking. "No. Nononono, the portal, the portal!"

She then sprinted out. "It would be too late! No no no!"

Flash walked out and yelled. "One 'No' would've been fine!"

The Doctor sighed and Flash shook his head. "Guess neither of us can get her."

Raising an eyebrow in confusion, the Doctor walked away. 'Well, that's a bother. I need that crown and fast. Maybe if the gym was fixed the dance will be back on.'

He then grinned. "Doctor, you are a genius!"

Author's Note

Right, next chapter is where the finale is taking place. We will be revealed who the voice in Sunsets head is as well as people finding out the Doctor.

Favourite, Follow, Review.

Safety and Peace, and may the Gods of Budder protect you